A Clever Connection

When reading through the works of those who study the SRP pathway, it becomes clear that these scientists have tremendous respect for the subject of their research. There are no complaints about the system being jury-rigged, a hodgepodge, or messy. On the contrary, as we have come to better understand how this system works, the researchers are under the impression that it is a very sophisticated system. It has been independently described as an “elegant pathway,” [24] an “elegant mechanism,” [25] and “a very elegant solution” [26]. We can likewise get a feel for the way scientists greatly respect the sophistication of this system by considering some excerpts from their studies. One team of researchers notes that “structural studies suggest that the relative position of the N and GTPase domains change during the targeting cycle in response to external cues and serves as an important indicator of the status of the protein” [13]. They also observe ”it appears that two half-reactions (binding of the signal peptide and assembly or activation of the translocon) must be monitored independently and then brought together before a translocation event can be initiated.” Another team notes, “targeting involves a series of ordered steps in which cargo binding and release must occur at the proper stages. Each of the conformational changes in the GTPase domains of the SRP and SR described above provides a potential point at which such control can be exerted, thereby coordinating the loading and unloading of cargoes” [27]. A team of reviewers comments that an “intrinsic advantage of cotranslational protein targeting is that the coupling of translation and translocation should prevent misfolding of the nascent chain in the cytoplasm” [9]. And yet another set of SRP researchers comment on the way the M domain interacts with the NG domain after binding of the signal sequence, observing that this “would elegantly link signal sequence binding to the M domain with GTP binding to the G protein” [10]. The same researchers also describe the central role of the particle protein (SRP54): “SRP function relies on the tightly controlled communication of SRP54 with the external regulators (e.g., the ribosome, the SR, and the translocon) and on internal communication between the domains of SRP54.” Since “the efficiency and fidelity of the targeting process are crucial for maintaining the remarkable organization that is essential for life” [16], it is not surprising that such an elegant and logical system would have been put into place to carry out the task.

Yet there is a better way to appreciate the inherent rationality of this system. In The Design Matrix: A Consilience of Clues, I argued that an engineered system should succumb to structural and functional decomposition. Because the SRP system is so relatively simple, and has been the subject of a good deal of research, it should be possible to cleanly decompose it. As can be seen from the figure below, I was easily able to break down the SRP system into a discrete set of eight functions.

Functional Decomposition of the SRP Pathway.

Each function, in turn, depends on distinct components of the system. The SCAN function occurs when the N domain from the particle protein interacts with ribosomal protein L23 and surveys the amino acid chain that emerges from the exist tunnel. If a signal emerges, the BIND function kicks in, where the M and N domains attach to the signal sequence creating a tight interaction between the SRP and the ribosome. The BIND function also results in a conformational change in the SRP, exposing the G-domain such that it can now bind GTP, causing the PRIME function to be activated. Once the PRIME function is activated, the SRP is licensed to interact with the receptor. In eukaryotes, the SRP contains the Alu domain which then interacts with the ribosome to PAUSE protein synthesis. Once both the SRP and receptor are primed, they can now DOCK through the interactions of their respective N and G domains. This docking not only activates the breakdown of the GTP molecules, but triggers the TRANSFER function, where the M domain (and perhaps the RNA) guides the signal sequence to the translocon. Once handed off, the THREAD function is carried out, as the ribosome resumes protein synthesis where the exit tunnel of the ribosome and the central pore of the translocon show “perfect alignment,” [9] so that the amino acid chain emerging from the exit tunnel is guided immediately into the membrane channel formed by the translocon (SecY). Finally, after GTP is hydrolyzed, the RELEASE function is implemented, whereby the SRP and receptor dissociate and now exist in forms that must be primed again to start the whole cycle over again.

The rationality of this system goes beyond the ability to structurally and functionally decompose it. Embedded within this system is a logical circuit that cycles the SRP in a unidirectional pattern, guided by the binding and then breakdown of GTP. The translocon is strategically plugged into this system for just long enough to receive the ribosome. What’s more, the PAUSE step is likewise strategically positioned such that bacteria, which apparently do not require it [9], can skip it and proceed directly to the DOCK function. In eukaryotes, where protein synthesis is paused, the THREAD function could likewise be re-labeled RESUME. That bacteria do not require the PAUSE function is intriguing. In bacteria, the process of transcription and translation are usually coupled such that the ribosome is translating the RNA that is still in the process of being synthesized by the RNA polymerase. Given that this linked process occurs near the membrane when membrane proteins are being synthesized [30], it suggests no PAUSE function is required, as the ribosome would already exist in the vicinity of the translocon and could be shuttled there almost instantly. In fact, there are data that show that the receptor itself can bind DNA and that such DNA binding stimulates the GTP hydrolysis activity of the receptor [31]. All of this suggests a sophisticated relationship between transcription, translation, and membrane protein insertion mediated by localization and the interaction between specific machine parts, where it is possible at least some membrane proteins may be inserted into the membrane while the genes for those proteins are still in the process of being transcribed [32]. One couldn’t ask for a more rational explanation for the missing PAUSE function in the bacterial SRP system. On the other hand, since eukaryotes have a nucleus that separates the process of transcription and translation, the need for a PAUSE makes sense, as SRP needs time to dock the ribosome to a distant membrane.

When everything is considered together, it is hard to imagine how this system could be any more rational. It has impressed the researchers who study it, demonstrates efficiency, flexibility, and sophistication, and is so logical that is nicely breaks down into a design flowchart of discrete functions.